The problem is that Aurora assumes that certain js files will exist and alters a few things about them. On some pages if one or more of these js files is removed by a Drupal module, it will result in a lot of notices. The fix is to check that the js Aurora wants to alter actually exists before doing so.

@googletorp, all of those javascript files should always be present... as they are required by Drupal core. I think some of the most recent code to the dev branch fixes this, but I am doing some more testing first.